R Graphical Manual

Last data update: 2014.03.03

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R Release (3.2.3)
CranContrib
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Classification

Results 1 - 10 of 53 found.
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AffyBatch-class (Package: affy) : Class AffyBatch

This is a class representation for Affymetrix GeneChip probe level data. The main component are the intensities from multiple arrays of the same CDF type. It extends eSet.

● Data Source: BioConductor
● Keywords: classes
● Alias: $.AffyBatch, AffyBatch, AffyBatch,ANY, AffyBatch-class, [,AffyBatch-method, [<-,AffyBatch-method, [[,AffyBatch-method, bg.correct,AffyBatch,character-method, boxplot,AffyBatch-method, cdfName, cdfName,AffyBatch-method, checkValidFilenames, col,AffyBatch-method, computeExprSet,AffyBatch,character,character-method, dim,AffyBatch-method, exprs,AffyBatch-method, exprs<-,AffyBatch,ANY-method, featureNames,AffyBatch-method, featureNames<-,AffyBatch-method, geneNames, geneNames,AffyBatch-method, geneNames<-, geneNames<-,AffyBatch,ANY-method, getCdfInfo, getCdfInfo,AffyBatch-method, hist,AffyBatch-method, image, image,AffyBatch-method, indexProbes, indexProbes,AffyBatch,character-method, indexProbes,AffyBatch,missing-method, indexProbes,AffyBatch-method, initialize,AffyBatch-method, intensity, intensity,AffyBatch-method, intensity<-, intensity<-,AffyBatch-method, length,AffyBatch-method, mm,AffyBatch-method, mm<-,AffyBatch,ANY-method, mmindex, mmindex,AffyBatch-method, pm,AffyBatch-method, pm<-,AffyBatch,ANY-method, pmindex, pmindex,AffyBatch-method, probeNames,AffyBatch-method, probes, probes,AffyBatch-method, probeset, probeset,AffyBatch-method, row,AffyBatch-method, se.exprs,AffyBatch-method, se.exprs<-,AffyBatch-method, show,AffyBatch-method, updateObject,AffyBatch-method
● 0 images

AffyRNAdeg (Package: affy) : Function to assess RNA degradation in Affymetrix GeneChip data.

Uses ordered probes in probeset to detect possible RNA degradation. Plots and statistics used for evaluation.

● Data Source: BioConductor
● Keywords: hplot, manip
● Alias: AffyRNAdeg, plotAffyRNAdeg, summaryAffyRNAdeg
● 1 images

MAplot (Package: affy) : Relative M vs. A plots

Create boxplots of M or M vs A plots. Where M is determined relative to a specified chip or to a pseudo-median reference chip.

● Data Source: BioConductor
● Keywords: hplot
● Alias: MAplot, MAplot,AffyBatch-method, Mbox, Mbox,AffyBatch-method, ma.plot
● 5 images

ProbeSet-class (Package: affy) : Class ProbeSet

A simple class that contains the PM and MM data for a probe set from one or more samples.

● Data Source: BioConductor
● Keywords: classes
● Alias: ProbeSet-class, barplot,ProbeSet-method, colnames,ProbeSet-method, express.summary.stat,ProbeSet,character,character-method, mm,ProbeSet-method, mm<-,ProbeSet,matrix-method, pm,ProbeSet-method, pm<-,ProbeSet,matrix-method, sampleNames,ProbeSet-method, show,ProbeSet-method
● 0 images

ProgressBarText-class (Package: affy) : Class "ProgressBarText"

A class to handle progress bars in text mode.

● Data Source: BioConductor
● Keywords: classes
● Alias: ProgressBarText-class, close,ProgressBarText-method, initialize,ProgressBarText-method, open,ProgressBarText-method, updateMe, updateMe,ProgressBarText-method
● 0 images

affy-deprecated (Package: affy) : Deprecated functions in package sQuote{affy

These functions are provided for compatibility with older versions of affy only, and will be defunct at the next release.

● Data Source: BioConductor
● Keywords:
● Alias: loess.normalize, maffy.normalize, multiloess, simplemultiLoess
● 0 images

affy-options (Package: affy) : Options for the affy package

Description of the options for the affy package.

● Data Source: BioConductor
● Keywords: manip
● Alias: affy-options
● 0 images

affy.scalevalue.exprSet (Package: affy) : Scale normalization for expreSets

Normalizes expression values using the method described in the Affymetrix user manual.

● Data Source: BioConductor
● Keywords: manip
● Alias: affy.scalevalue.exprSet
● 0 images

barplot.ProbeSet (Package: affy) : show a ProbeSet as barplots

Displays the probe intensities in a ProbeSet as a barplots

● Data Source: BioConductor
● Keywords: hplot
● Alias: barplot.ProbeSet
● 4 images

bg.adjust (Package: affy) : Background adjustment (internal function)

An internal function to be used by bg.correct.rma.

● Data Source: BioConductor
● Keywords: manip
● Alias: bg.adjust, bg.parameters
● 0 images